Modify node regularization in kinetic families.

rmgpy/data/kinetics/family.py

@@ -3791,10 +3791,17 @@ def simple_regularization(self, node, template_rxn_map, test=True):
 
         if isinstance(node.item, Group):
             indistinguishable = []
+
+            if node.children==[]: #if this is a leaf node, run it through get_extension_edge so that the regularization info is passed to leaf node
+                print('extending leaf nodes to get regularization info')
+                _, _ = self.get_extension_edge(node, template_rxn_map, obj=None, T=1000.0, iter_max=1, iter_item_cap=1)
+
             for i, atm1 in enumerate(grp.atoms):
 
                 skip = False
-                if node.children == []:  # if the atoms or bonds are graphically indistinguishable don't regularize
+                if node.children == []:  
+
+                    # if the atoms or bonds are graphically indistinguishable don't regularize
                     bdpairs = {(atm, tuple(bd.order)) for atm, bd in atm1.bonds.items()}
                     for atm2 in grp.atoms:
                         if atm1 is not atm2 and atm1.atomtype == atm2.atomtype and len(atm1.bonds) == len(atm2.bonds):

rmgpy/molecule/group.py

@@ -1571,7 +1571,7 @@ def get_extensions(self, r=None, r_bonds=None, r_un=None, basename='', atm_ind=N
         """
         cython.declare(atoms=list, atm=GroupAtom, atm2=GroupAtom, bd=GroupBond, i=int, j=int,
                        extents=list, RnH=list, typ=list)
-
+        
         extents = []
         if r_bonds is None:
             r_bonds = [1, 1.5, 2, 3, 4]
@@ -1726,6 +1726,8 @@ def specify_atom_extensions(self, i, basename, r):
 
         grps = []
         Rset = set(r)
+
+        #consider node splitting        
         for item in r:
             grp = deepcopy(self)
             grpc = deepcopy(self)
@@ -1751,6 +1753,32 @@ def specify_atom_extensions(self, i, basename, r):
             grps.append(
                 (grp, grpc, basename + '_' + str(i + 1) + old_atom_type_str + '->' + item.label, 'atomExt', (i,)))
 
+        #generate an extension without node splitting
+        if len(self.atoms[i].atomtype)>len(Rset):
+            print('generating a non-splitting extension')
+            if all(r in self.atoms[i].atomtype for r in Rset): 
+                #that means even if we update the atomtype of the atom to the Rset, it will still be a specification
+                grp = deepcopy(self)
+                grp.atoms[i].atomtype = list(Rset)
+
+                #rename
+                old_atom_type = grp.atoms[i].atomtype
+
+                if len(old_atom_type) > 1:
+                    labelList = []
+                    old_atom_type_str = ''
+                    for k in old_atom_type:
+                        labelList.append(k.label)
+                    for p in sorted(labelList):
+                        old_atom_type_str += p
+                elif len(old_atom_type) == 0:
+                    old_atom_type_str = ""
+                else:
+                    old_atom_type_str = old_atom_type[0].label
+
+                grps.append(
+                (grp, None, basename + '_' + str(i + 1) + old_atom_type_str + '->' + ''.join(r.label for r in Rset), 'atomExt', (i,)))
+
         return grps
 
     def specify_ring_extensions(self, i, basename):